Download Complete genome determination and analysis of Acholeplasmataceae Acholeplasma oculi

Complete genome determination and analysis of
Acholeplasma oculi strain 19L, highlighting the loss
of basic genetic features in the Acholeplasmataceae
Christin Siewert1
Email: [email protected]
Wolfgang R Hess2
Email: [email protected]
Bojan Duduk3
Email: [email protected]
Bruno Huettel4
Email: [email protected]
Richard Reinhardt4
Email: [email protected]
Carmen Büttner1
Email: [email protected]
Michael Kube1*
*
Corresponding author
Email: [email protected]
1
Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute,
Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany
2
Genetics & Experimental Bioinformatics, University of Freiburg, Institute of
Biology III, Schänzlestraße 1, 79104 Freiburg, Germany
3
Institute of Pesticides and Environmental Protection, Banatska 31b, P.O. Box
163, 11080 Belgrade, Serbia
4
Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne,
Germany
Abstract
Background
Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera
Acholeplasma and ‘Candidatus Phytoplasma’. Acholeplasmas are ubiquitous saprophytic
bacteria. Several isolates are derived from plants or animals, whereas phytoplasmas are
characterised as intracellular parasitic pathogens of plant phloem and depend on insect
vectors for their spread. The complete genome sequences for eight strains of this family have
been resolved so far, all of which were determined depending on clone-based sequencing.
Results
The A. oculi strain 19L chromosome was sequenced using two independent approaches. The
first approach comprised sequencing by synthesis (Illumina) in combination with Sanger
sequencing, while single molecule real time sequencing (PacBio) was used in the second. The
genome was determined to be 1,587,120 bp in size. Sequencing by synthesis resulted in six
large genome fragments, while the single molecule real time sequencing approach yielded
one circular chromosome sequence. High-quality sequences were obtained by both strategies
differing in six positions, which are interpreted as reliable variations present in the culture
population. Our genome analysis revealed 1,471 protein-coding genes and highlighted the
absence of the F1FO-type Na+ ATPase system and GroEL/ES chaperone. Comparison of the
four available Acholeplasma sequences revealed a core-genome encoding 703 proteins and a
pan-genome of 2,867 proteins.
Conclusions
The application of two state-of-the-art sequencing technologies highlights the potential of
single molecule real time sequencing for complete genome determination. Comparative
genome analyses revealed that the process of losing particular basic genetic features during
genome reduction occurs in both genera, as indicated for several phytoplasma strains and at
least A. oculi. The loss of the F1FO-type Na+ ATPase system may separate
Acholeplasmataceae from other Mollicutes, while the loss of those genes encoding the
chaperone GroEL/ES is not a rare exception in this bacterial class.
Background
Acholeplasma species comprise bacteria of the family Acholeplasmataceae in the class
Mollicutes, characterised by the lack of sterol requirement for growth and thereby separated
from Mycoplasmataceae and Spiroplasmataceae [1]. The majority of Acholeplasma spp. are
described as saprophytes and commensals. An evident assignment as pathogens is hampered
by the fact that several Acholeplasma spp. are distributed ubiquitously. Moreover, no primary
pathogen is described for this genus. However, the isolation of strains from diseased animals,
and classification as putative animal pathogens, applies to species such as A. axanthum and A.
oculi [2,3]. This assignment of the type strain A. oculi 19L (syn. A. oculusi) was the result of
its isolation from goat eyes infected with keratoconjunctivitis and re-infection experiments
[2]. However, the assignment of A. oculi to this disease is rare in contrast to several
Mycoplasma spp. [4].
Besides Acholeplasma, the Acholeplasmataceae family also includes the provisory taxon
‘Candidatus Phytoplasma’. Phytoplasmas are associated with several hundred plant diseases
– and thus significant economic losses [5]. After insect vector-mediated transmission,
phytoplasmas colonise as intracellular obligate parasites the sieve cells of a plant, often
resulting in abnormal growth and reduced vitality. No general evidence for pathogenesis by
acholeplasmas in colonised insects and plants has been provided to date. However, a recently
published study on the A. laidlawii strain PG-8 supports its phytopathogenicity, which can be
increased after nanotransformation in ultramicroform cells and might be correlated to
extracellular vesicle formation under experimental conditions [6]. Further studies are needed
in this respect, but the results may indicate a mechanism shared by both genera. In contrast,
experimentally proven effector proteins or membrane proteins involved in phytoplasma-host
interaction were not identified in the acholeplasmas [7]. These genetic elements of
phytoplasmas might have originated from horizontal gene transfers. Massive gene loss, in
combination with duplication events and genome instability, separates the phytoplasmas from
the acholeplasmas. The complete genome sequences of eight strains of this family have been
published, comprising the acholeplasmas A. laidlawii strain PG-8A [8], A. brassicae strain
O502 and A. palmae strain J233 [7] and the phytoplasmas ‘Ca. P. australiense’ strain rp-A [9]
and NZSb11 [10], ‘Ca. P. asteris’ strain OY-M [11] and AY-WB [12] and ‘Ca. P. mali’ strain
AT [13]. In the past, all five phytoplasma strains and A. laidlawii were sequenced by
applying the whole genome shotgun approach and using plasmid or fosmid libraries as
templates for dye-terminator sequencing (Sanger sequencing). In determining the
chromosome sequences of A. brassicae and A. palmae, a combination of Sanger sequencing
and next generation sequencing methods (pyrosequencing, 454 Life Sciences/Roche) was
applied for the first time to this bacterial family [7].
Both taxa show characteristic gene losses. In comparison to acholeplasmas, phytoplasmas
lack the F1FO ATPase synthetase complex, the cell division protein FtsZ, a wider variety of
ABC transporters, the Rnf complex and the membrane protein SecG of the Sec-dependent
secretion system. Moreover, acholeplasmas possess a rich repertoire of enzymes involved in
carbohydrate metabolism, fatty acids, isoprenoids and partial amino acid metabolism [7].
Because these findings were inferred from the analyses of three acholeplasma and five
phytoplasma genome sequences, it remains unclear as to what extent these differences
between the two genera can be truly generalised or if the other acholeplasmas might share
some of these features of their genetic repertoire with the phytoplasmas. Therefore, we
determined the complete genome of A. oculi strain 19L by applying two different strategies
based on sequencing by synthesis (SBS, Illumina) and, in a second approach, single molecule
real time (SMRT, PacBio) sequencing. The subsequent analyses highlight the efficiency of
current sequencing technologies and provide remarkable insights into the evolution of
Acholeplasmataceae.
Results
Comparison of assemblies derived from SBS and SMRT sequencing
The SBS and SMRT approaches enabled the efficient reconstruction of the complete genome
sequence in independent experiments. SBS sequencing provided 1,095,574 paired-end quality
passed reads with an average length of 101 nt (total read length of 110,652,974 nt). De novo
assembly of the SBS-derived reads alone led to the incorporation of 964,613 reads (88%) into
six large contigs (513260 bp, 244477 bp, 109253 bp, 547590 bp, 106516 bp and 52461 bp in
size), showing a 64-fold read coverage on average (Table 1, Figure 1) and reaching a total
contig length of 1,573,557 bp. In turn, the mapping of SBS reads on the finished genome
sequence revealed no uncovered regions. Gap regions derived from the SBS de novo
assembly cover repetitive sequences of high similarity. In detail, two gaps (4,748 bp and
4,898 bp in size) include the rRNA operon regions (99% sequence identity), two gaps (1,661
bp each) include two transposases (100% sequence identity), one gap (186 bp) borders
Acholeplasma phage L2 (>92% sequence identity) and the smallest gap (176 bp) is located
close to a heavy metal translocating P-type ATPase (92% sequence identity). Gaps derived
from the assembly of SBS reads were closed by primer-walking (Sanger sequencing),
resulting in a complete circular chromosomal sequence.
Table 1 Results obtained by the de novo assembly of paired-end SBS reads
Name
contig1
contig2
contig3
contig4
contig5
contig6
total
Consensus length [bp]
513,260
244,477
109,253
547,590
106,516
52,461
1,573,557
Total read count
287,207
159,855
78,395
331,384
77,108
30,664
964,613
Average coverage
56.16
65.63
72.03
60.74
72.65
58.65
64.31
Figure 1 Genome circle of Acholeplasma oculi strain 19L and a summary of the
comparative analyses. Circular patterns (from outside to inside): 1 (outer circle), scale in
base pairs of the chromosome; 2 (blue), six contigs obtained from the initial SBS paired-end
read assembly; 3 (red), 28 differences identified by comparing the results of the Illumina and
PacBio sequencing results; 4 (black), predicted proteins encoded on the forward and reverse
strands; 5 (green) tRNA genes and (grey) rRNA operons; 6 (violet), predicted unique proteins
for A. oculi in comparison to other Acholeplasmataceae species; 7 (orange), orthologous
proteins of A. oculi and A. laidlawii; 8 (light orange), orthologous proteins of A. oculi and A.
brassicae; 9 (yellow), orthologous proteins of A. oculi and A. palmae; 10-14 (green),
orthologous proteins of A. oculi and ‘Ca. P. asteris’ strain OY-M, AY-WB, ‘Ca. P.
australiense’ strain rp-A, NZSb11 or ‘Ca. P. mali’ strain AT, respectively; 15 (olive and
purple), cumulative G + C skew.
The SMRT sequencing approach provided 42,300 SMRT reads with a mean read length of
6,747 nt (total read length of 285,414,973 nt). A total of 38,875 reads enabled the gapless
reconstruction of the circular chromosome at a size of 1,587,116 bp. A consensus
concordance of 99.9991% and 144.1-fold average sequence coverage were reached. Around
8% of the SMRT-derived reads were rejected due to insufficient quality or incomplete read
processing during the assembly.
Apart from the 14 kb size difference in the total contig length obtained by the two methods, it
is remarkable that only 28 positions differ, concerning 31 bases in total (Table 2). Amplifying
these positions, and re-sequencing by Sanger, led to the unambiguous assignment of 22
positions. In addition, the results indicated the presence of six polymorphic positions. Thus,
both approaches enabled the efficient reconstruction of the complete chromosome sequence.
The final sequence is in accordance with the results obtained through the Sanger sequencing
of PCR products covering the ambiguous regions. Consequently, only polymorphisms
occurring at high frequency in one PCR template were detected as double peaks in the
chromatograms. We conclude that the majority of differences indicate that polymorphisms
were already present in the original cell population. Furthermore, one of the substitutions
results in a non-synonymous exchange (Aocu_13520/ rpsE) within the 30S ribosomal protein
S5, while three substitutions result in synonymous base exchanges (Aocu_08380,
Aocu_10040/ mutS, Aocu_14610) and two positions are located in intragenic regions. A high
incidence of differences (14 nucleotides, Table 2) was identified within a putative phageassociated region (position 972,742-977,480), which may undergo rapid degradation and
comprises an integrase (Aocu_08840) and fragments of a restriction-modification system
(truncated restriction endonuclease, Aocu_08860; truncated restriction endonuclease,
Aocu_08870 and hsdM, Aocu_08880).
Table 2 Evaluation of differences by PCR and Sanger sequencing
Primer
Aocu1FS1
Aocu1RS1
Aocu2FS2
Aocu2RS2
Aocu3FS3
Aocu3RS3
Aocu45FS4
Aocu45RS4
Aocu6FD5
Aocu6RD5
Aocu7FS6
Aocu7RS6
Aocu8FS7
Aocu8RS7
Aocu910FS8
Aocu910RS8
Aocu11FS9
Aocu11RS9
Aocu12-FDI10
Aocu12-RDI10
Sequence 5′- 3′
No. of differences Position of the conflict SMRT SBS Sanger
ACGCAATTTTGAATGCGAGTC
1
29,164
A
G
G
AAGCGCCACCCATCTTTACA
TCCAAGATCAACCGTTGGAACA
1
45,841
C
T
T
TCTTTGTGCCTCACCACCTG
GGCAGTTGGTACAAGAGCGA
1
94,414
A
C
C
AAATTCCGGTGGTGGTACGG
ACAGTTGATGGAAGCTATGAAGG
2
227,147
A
C
C
ACGGTTGTTGGGAATCATGG
228,403
A
G
G
ACTGCAGCTAATCCAACGGA
1
332,224/5
G
TTCAAGTGTTCCACGTCGGT
TCAGCATCCGGTTATGCTCC
1
460,047
G
A
A
GTTGGATGCCACTCGAAGGA
TCTTGTCTTGACCACCCCAA
1
584,955
A
G
G
CAGCAAGTGTTTGACTCGCA
AAATCAGTTGCTGCATTAAGAGGT
2
904,938
G
C
S*
ACTGGGAGTATCGATTGCAGG
904,961
C
A
M*
TTAGATAGTGCGGCAAGGGG
1
927,019
G
A
R*
AACGCACCGAATCATTTCGC
GTCGATGCGCAAGCATAACC
4
972,742/3
T
TCTAGGAGGAACACCATCACG
974,678/9
-AG AG
974,999/975,000
-CT CT
975,166/7
-AG AG
Aocu16-22FDI11 TGCTAGCTGACCTTATGGGAC
7
976,093/4
T
976,419
A
A
Aocu16-22RDI11 GACGTTTAGGCGAAGTAGTCG
976,451/2
T
976,520/1
G
976,525
T
T
976,634/5
T
977,480
T
T
Aocu23FS12
GCAATACGACCAACCAAGCG
1
1,091,760
T
C
Y*
Aocu23RS12
AATGCGCCAATTCCAAAACG
Aocu24FS13
GACCAACGTTTCTCGCATGG
1
1,410,995
A
G
G
Aocu24RS13
TGACCACTTAGGTAATCGTCGT
Aocu25FS14
AACTTGGTCCATGTGCCTCT
1
1,443,728
A
G
G
Aocu25RS14
ATGAGGCTACCATTACCCGC
Aocu26FS15
ACCTCGATTGTTCCACCAGC
1
1,471,015
C
T
Y*
Aocu26RS15
AAGTGCTCGCTTACGTCTGG
Aocu278FSI16 TTGCTTGGTTAGCTCCTCCC
2
1,576,028
T
A
W*
Aocu278RSI16 TAGGTGTGCGTCCTGAAGGT
1,577,778
T
T
Sixteen primer pairs were designed for the PCR and Sanger sequencing of 28 different regions resulting from the SMRT
(PacBio) and SBS (Illumina) approaches. Primer pairs, numbers of identified differences, positions in the submitted
sequence, SMRT- and SBS-determined sequences in any particular position are provided in addition to the Sanger
sequencing results derived from the PCR product. Ambiguous results obtained by Sanger sequencing (*) were interpreted
from the sequencing chromatograms.
In summary, Sanger sequencing confirmed the SBS-derived sequences for 22 out of 28
differences. The deviating SMRT data at these positions may indicate errors or rare sequence
variations within the final chromosome sequence of 1,587,120 bp. Polymorphic sites at six
sequence positions of the chromosome are supported by SMRT assembly, deviating SBS
reads and Sanger sequencing.
Benchmarks of the genome of A. oculi and its comparison to other
Acholeplasmataceae
The finished consensus sequence of A. oculi strain 19L consists of 1,587,120 bp encoding
two rRNA operons, 34 tRNA genes and 1,471 predicted protein coding genes (Table 3). A.
laidlawii strain PG-8A is the closest known relative of A. oculi strain 19L, which is supported
by the construction of the phylogenetic tree (Figure 2). This close relationship is also
reflected by the prediction of 1,068 shared proteins (77%) compared to 866 (60%) and 973
(57%) proteins shared with A. brassicae strain O502 and A. palmae strain J233 (Figure 3).
The predicted core of the four Acholeplasma spp. consists of 703 proteins and the calculated
pan-genome comprises 2,867 proteins in total (Figure 4). The highest number of unique
proteins (570) possesses A. brassicae, which also exhibits the largest genome in this family
(1,877,792 bp, 1,704 protein coding genes, Table 3).
Table 3 Overview of the currently completely determined Acholeplasmataceae genomes
Genus
Acholeplasma
Species
oculi
laidlawii brassicae palmae
mali
Strain
19L
PG-8
0502
J233
AT
circular
circular
linear
chromosome organization circular circular
size [bp]
1,587,120 1,496,992 1,877,792 1,554,229 601,943
31.93
35.77
29,98
21.39
G + C [%]
31.29
CDS
number (pseudogenes)
1,380 1,704 (14) 1,441 (2) 497 (15)
1,471
G + C [%]1
32.23
36.15
29.20
22.60
31.49
984
1,003
979
957
average length1
992
coding percentage1 [%]
90.7
90.3
90.6
76.6
92.0
rRNA
number
6
14
6
6
6
G + C [%]
48.57
49.31
48.64
44.32
49.27
tRNA
number
34
45
35
32
34
G + C [%]
56.97
56.12
56.56
52.41
56.87
plasmdis
number
CP
FO
FO
CU
LK
000896
681348
681347 469464
acc. no.
028559
[8]
[7]
[7]
[13]
this study
Bold letters highlight results obtained in this study. 1excluding pseudogenes.
‘Candidatus Phytoplasma’
australiense
asteris
rp-A NZSb11 OY-M AY-WB
circular circular circular circular
879,959 959,779 853,092 706,569
27.42
27.19
27.76
26.89
839 (155)
28.72
825
64.1
1100
28.47
674
77.3
752
29.09
829
73.1
671
28.54
776
73.7
6
46.37
6
46.61
6
45.95
6
46.14
35
54.11
35
54.11
32
53.61
31
53.6
1
AM
422018
[9]
1
2
4
CP
AP
CP
002548 006628 000061
[10]
[11]
[12]
Figure 2 Phylogenetic tree based on 16S rRNA gene sequences of acholeplasmas
(orange) and phytoplasmas (green). The tree was calculated by employing the maximum
likelihood algorithm and bootstrap calculation for 1,000 replicates (only values of at least
70% are shown). The bar indicates 0.05 substitutions per nucleotide. The accession numbers
are given in parentheses. Mycoplasma genitalium strain G37 is set as an out-group. Species
with complete chromosomes available are shown in bold. Roman numerals are given
according to acholeplasma clades [14]. The coloured boxes indicate that gene encoding F1F0
Na+ ATP synthase (light blue), V1VO Na+ ATP synthase (yellow), V1VO H+ ATP synthase
(dark blue), GroEL (red) or SecB (violet) are present (limited to complete genome
sequences).
Figure 3 Bar chart of shared protein content. The total number of annotated protein
coding genes (lighter part) for each complete genome sequence is given, together with the
number and percentage of orthologous proteins with A. oculi in the lower part of each bar
(darker part). PanOCT was used to predict orthologous proteins.
Figure 4 Four-set Venn diagram of the pan-genome of the genus Acholeplasma based on
the prediction of orthologous proteins by PanOCT. Each ellipse shows in sum the total
number of coding sequences of one Acholeplasma species. Intersections indicate predicted
shared content.
Only a basic set of proteins is shared between A. oculi and the five complete phytoplasma
genomes. The 293 to 310 predicted shared proteins (27% to 59%) are consistent with
previously calculated numbers for other acholeplasmas [7,8] (Figure 3). The second highest
number of unique proteins (440) is predicted for A. palmae (Figure 4), which is the closest
known relative of the phytoplasmas [7] (Figure 2) and is also supported by the highest
number of predicted shared proteins with the five completely sequenced phytoplasmas
(Additional file 1). In second position among the acholeplasmas, A. oculi shares many of its
proteins with the phytoplasmas, supported by its phylogenetic assignment and the received
PanOCT results. This analysis is also supported by A. oculi and A. laidlawii, which share the
highest number of proteins amongst the acholeplasmas (Figure 3). The phytoplasmas’
genome reduction process is reflected by the low number of 294 proteins assigned to the
shared core within the pan-genome (2,077 proteins in total; Figure 5). Phytoplasma genomes
are characterised by extensive gene losses, transposon-mediated gene duplication [12] and
horizontal gene-integration events [15]. Comparing the pan-genomes of acholeplasmas and
phytoplasmas, Venn analysis highlights basic differences in the overall gene content.
Complete Acholeplasma and ‘Ca. Phytoplasma’ genomes collectively encode 402 and 14
predicted unique proteins, respectively (Figure 6, Additional file 2). The 14 unique genes,
which are common to the genus ‘Ca. Phytoplasma’, encode nine hypothetical proteins and
five proteins with known functions. Two of the hypothetical proteins contain a sequencevariable mosaic (SVM) motif [16] and comprise SAP05 (AYWB_032), which is described as
a putative effector protein [17] inducing the formation of smooth young rosette leaves that
lack serrations along the leaf margin [18], and SAP30 (AYWB_402), which is similar to
SAP11 containing an eukaryotic nuclear localisation signal [19,20]. This group of unique
genes also includes two phytoplasma proteins involved in a suggested alternative pathway in
the carbohydrate metabolism of phytoplasmas [7,13,21]. The malate/Na + symporter (MleP)
provides a carbon source which undergoes oxidative decarboxylation by malate
dehydrogenase (SfcA), thereby providing pyruvate processed by the dehydrogenase
multienzyme complex and providing acetyl coenzyme A. The phosphotransacetylation of
acetyl-CoA performed by the PduL-like protein provides acetyl-phosphate, which is
processed via acetate kinase (AckA) and results in the formation of ATP and acetate. A. oculi
does not encode MleP, SfcA and the phosphate acetyltransferase (Pta), which is common in
mycoplasmas, though it is suggested that PduL fulfills this function in Acholeplasmataceae
[7,21] including A. oculi. However, the alternative energy-yielding pathway of phytoplasmas
utilising malate is clearly not encoded in the analysed acholeplasma genomes.
Figure 5 Five-set Venn diagram of the pan-genome of the genus ‘Ca. Phytoplasma’
based on the prediction of orthologous proteins by PanOCT. Each ellipse shows in sum
the total number of coding sequences of one strain. Intersections indicate predicted shared
content.
Figure 6 Composition of the Acholeplasma and ‘Ca. Phytoplasma’ core-genomes as
predicted by PanOCT. The total number of proteins inferred from the respective core
genome is given in the middle (uncoloured part).
Furthermore, the PanOCT analysis predicted that phytoplasmas encode unique AAA+
ATPase, thymidylate kinase and a DNA-dependent RNA polymerase sigma 70 factor RpoD
(IPR013325, IPR014284, IPR007627, Additional file 2). RpoD exhibits only insignificant
BlastP hits to acholeplasmas’ sigma factors (minimal e-value 9e-08, score 47), and no
ortholog was predicted via PanOCT. The existence of a phytoplasma-specific sigma factor
points towards some peculiarities in their regulatory system. The other two deduced proteins
showed similarities in BlastP analysis to some acholeplasma proteins, albeit they differed in
small domain structures. For instance, the AAA+ ATPase of phytoplasmas gave a hit to the
ATP-dependent zinc metalloprotease FtsH, which also contains the AAA+ domain structure,
and the thymidylate kinases of acholeplasmas showed an additional conserved site (predicted
by the PROSITE database search, http://prosite.expasy.org/) – contrary to the thymidylate
kinases of phytoplasmas. The overall high number of 402 unique proteins for the four
acholeplasmas is interpreted with respect to the diverse environments colonised by
acholeplasmas.
Particularities of A. oculi strain 19L
A high percentage (55% – 148) of the 271 proteins predicted to be ‘unique’ for A. oculi in the
Acholeplasmataceae are annotated as hypothetical proteins (Figure 1). This set of unique
proteins contains phage-related proteins similar to the Acholeplasma phage L2 [GenBank:
L13696.1] [22], including the proteins L2_7, L2_9, L2_11 and L2_12, and which are
organised in clusters at three different chromosome regions (118,599-126,732 Aocu_0117001290; 650,878-659,350 Aocu_05790-5880; 1,062,230-1,068,906 Aocu_09710-9810). In
addition, two recombinases (Aocu_08890, Aocu_13990), two integrases (Aocu_05790,
Aocu_08840) and one resolvase (Aocu_14000) belong to the list of unique proteins. Besides
phage-assigned elements, six transposases were identified, including a mutator type
(Aocu_01380), IS3/IS911 family protein (Aocu_01570), IS200-like (Aocu_03680),
IS204/IS1001/IS1096/IS1165 (Aocu_04230/50) and other transposon-related elements
(insertion element subunit, Aocu_03690). Furthermore, a putative complex transposon is
associated with a region carrying a high number of unique proteins (134,519-157,461,
Aocu_01380-01570). Beside other proteins, it encodes two oligopeptide ABC transporter
components (periplasmatic component oppA and ATP-binding protein oppD) and six
glycosyl hydrolase family proteins and a periplasmatic binding protein/LacI transcriptional
regulator. A second candidate for a complex transposon (423,889-490,302 Aocu_036804250) encodes a UDP-galactopyranose mutase (Glf, Aocu_04190) in addition to another Glf
(Aocu_04670) outside the proposed complex transposon. These genes set A. oculi apart from
other acholeplasmas. The UDP-galactopyranose mutase is involved in the conversion of
UDP-galactopyranose (UDP-GALP) into UDP-galactofuranose (UDP-GALF) (IPR004379),
which is the precursor to D-galactofuranose and is often found in the lipopolysaccharide O
antigens of several Gram-negative bacteria [23].
A. oculi is also separated from the other three acholeplasmas by the presence of a putative
manganese efflux pump (MntP, Aocu_03470), thereby enabling the exportation of
manganese ions, which are toxic in higher amounts. The functional relevance of MntP for
manganese homoeostasis has been demonstrated for E. coli [24]. The direct comparison of
the A. oculi and the E. coli MntP protein shows 31% identical and 56% similar residues. In
addition, A. oculi encodes a cadmium resistance transporter (CadD, Aocu_08600) and one
amidohydrolase (AmhX, Aocu_08940). In Bacillus subtilis, AmhX enables the cleavage of
the amide bond between non-active conjugated amino acids and may mobilise indole-3-acetic
acid (IAA) from inactive storage forms in plants besides several other functions [25]
(IPR017439 [26]). A. oculi was also detected on plant surfaces [27]. Therefore, one may
speculate whether A. oculi can stimulate the growth of colonised plant tissue. Hints for such a
manipulation of the IAA metabolism of plants have also been obtained for A. palmae and A.
brassicae encoding a putative auxin efflux carrier protein [7], though no experimental studies
are available.
A. oculi is separated from the other Acholeplasma spp. by encoding several additional
transcriptional regulators such as ubiC (Aocu_00680), gntR (Aocu_00690), Cro/C1 family
proteins (Aocu_01770, Aocu_05750, Aocu_08910 and Aocu_13020) and TetR family
proteins (Aocu_14450) not assigned to other Cro/C1-type or TetR family proteins in this
family. In total, A. oculi encodes 13 Cro/C1 family proteins, nine of which are shared, and
four TetR family proteins, one of which is shared by the other acholeplasmas.
Furthermore, A. oculi is separated from other Acholeplasmataceae by encoding the GDP-Dglycero-α-D-manno-heptose biosynthesis pathway providing D-glycero-D-manno-heptose
(HddA, GmhA, HddC, GmhB; Aocu_04590-620). This is a precursor of the inner core
lipopolysaccharide [28]. These proteins are similar to those found in the pathway that was
reconstructed for the Gram-positive bacteria Aneurinibacillus thermoaerophilus strain DSM
10155 (member of Bacillus/Clostridium group) [28]. For acholeplasmas, there is only one
report by Mayberry et al. [29] that A. modicum contains heptose among the glycolipids.
Moreover, A. oculi encodes two additional proteins, thus playing a role in the biosynthesis of
the amino acid methionine. MetW (Aocu_08790) synthesises methionine from homoserine
(IPR010743 [30]), which provides an additional pathway to produce methionine needed in
the initiation of translation. The diaminopimelate epimerase (DapF, Aocu_08990) belongs to
the aspartate pathway (IPR001653), from which the four amino acids lysine, threonine,
methionine and isoleucine can be synthesised.
All species of the Acholeplasmataceae encode a protein core for the Sec-dependent secretion
system (Ffh, FtsY, SecA, SecE, SecY and YidC), whereas the four analysed Acholeplasma
spp. additionally encode the membrane protein SecG. The chaperone SecB, which is only
encoded in A. laidlawii and A. oculi, binds the precursor protein and directs it to the SecA
protein. The function of SecB can also be fulfilled by the proteins DnaK and DnaJ [31],
which are encoded in all genome sequences of the family, or by GroEL and GroES [32]. A.
oculi lacks the common chaperone GroEL/ES (Figure 7), consistent with conclusions drawn
from the draft sequences of phytoplasma strains [33] and the analyses of other species in the
Mollicutes that these genes are not essential [34]. The complete genome sequences of the
Acholeplasmataceae encode the trigger factor (TF), dnaK, dnaJ, grpE and hrcA. Other heat
shock proteins, such as Hsp20, were not identified in A. palmae and ‘Ca. P. mali’. Hsp33 is
only identified in the acholeplasmas.
Figure 7 Locus tags of the encoded chaperons and heat shock proteins within the
Acholeplasmataceae. Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, ACL; A.
palmae, Apal; A. brassicae, Abra; ‘Candidatus P. mali’ strain AT, ATP; ‘Ca. P. australiense’
strain rp-A, PA; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M,
PAM; ‘Ca. P. asteris’ strain AY-WB, AYWB. Shared proteins are highlighted in blue.
Beside GroEL/ES, A. oculi lacks the complete gene set encoding the F1FO-type Na+ ATPase,
which was identified in A. laidlawii, A. brassicae and A. palmae (Figures 8 and 9). Therefore,
A. oculi, A. laidlawii and A. palmae encode one V-type Na+ ATPase. A. palmae differs in
gene content by encoding no atpC subunit for this ATPase. In addition, all genes encoding
the V1VO H+ ATPase are present in all four acholeplasma strains. Summing up, each
acholeplasma species possesses at least one full operon which encodes at least either one H+
or one Na+ ATPase system. The NtpG subunit, namely the rotated central stalk next to NtpD
and NtpC [35], is missing in all species. In contrast to the acholeplasmas, the F- and V-type
ATPases were not identified in phytoplasmas.
Figure 8 An overview of the subunits of the F- and V-type ATPases encoded by
acholeplasma genomes. The subunit order follows location within the chromosomes. Genes
shared by all of the four acholeplasmas are highlighted in blue. Numbers indicate locus tags
corresponding to the deduced proteins.
Figure 9 Alignment made by partial protein sequences of the F-type ATPase subunit c
(AtpE) and the V-type ATPase subunit K (NtpK). Assignments were made according to
Dzioba et al. [36]. Species are highlighted regarding their phylum assignment to Tenericutes
(red), Firmicutes (green) or others (violet). Superscripted numbers indicate position in protein
sequence. *UF = unknown function
Discussion
F1FO ATPases and V1VO ATPases are membrane complexes which function either as H+- or
Na+-translocators [37] (Figure 9). The F1FO ATPase consists of two units – the integral
membrane protein FO (atpBEF) acting as a proton channel and the peripheral catalytic stalk
F1 (atpHAGDC). The V1VO ATPase is built by the integral membrane protein VO (ntpIK) and
the peripheral catalytic stalk V1 (ntpECFABD) [38]. The difference between both transporters
is that the V-type ATPase only works in one direction by hydrolysing ATP to produce either
a proton or a sodium motive force, while additionally the F-type ATPase is able to act in the
other direction by allowing the regulation of the cellular ion pool using the proton motive
force, which leads to ATP generation [39].
Following the sequence-based prediction of Dzioba et al. [36], the classification of the ion
translocating profile can be inferred from the alignment of the protein sequences of the
subunits AtpE (F-type ATPase) and NtpK (V-type ATPase). Certain conserved binding
motifs are represented by the amino acids at specific positions, in order to specify an H+- or a
Na+-translocation (Figure 9). As a result, one F1FO-type Na+ ATPase is suggested to be
encoded by all acholeplasmas except for A. oculi, and one V-type Na+ ATPase is predicted
for all acholeplasmas except for A. brassicae. It remains unclear as to whether the V-type Na+
ATPase of A. palmae is working despite the lack of an atpC subunit, although this species
additionally encodes the F1FO-type Na+ ATPase. Moreover, protein sequence alignment leads
to the conclusion that all acholeplasmas encode one V-type H+ ATPase. Deductively, all
acholeplasmas encode at least one Na+ and one H+ translocator. This finding stands in
accordance with the evidence that Acholeplasma laidlawii strain B possesses a (Na+-Mg2+)ATPase which is capable of actively extruding sodium ions against the concentration gradient
[40]. This previously described, but not genetically characterised, cation pump was linked to
the characteristically low intracellular sodium level of these bacteria.
Ultimately, the loss of the F1FO-type Na+ ATPase in Acholeplasmataceae, as is the case for A.
oculi, may probably be compensated by the V-type Na+ ATPase. The loss of this genetic
module in phytoplasmas remains unclear, but it might be interpreted in respect to the
adaptation of phytoplasmas in the intracellular environment with constant osmotic conditions.
The comparison of both V-type ATPase operons encoded by A. oculi highlights low sequence
identities of the involved proteins (24% to 52%) and differences in protein lengths (Figure 9).
This leads to the suggestion that the operons did not derive from a duplication event.
Besides F1FO ATPase, the loss of groEL/ES is remarkable. Native protein folding is
conducted by molecular chaperones such as GroEL/ES (Hsp60), DnaK (Hsp70), DnaJ, GrpE,
SecB and other heat-shock proteins (Hsp) [41]. GroEL complexes (800 kDa) consisting of
two stacked heptameric rings exhibit ATPase activity [42]. The smaller GroES (10 kDa),
together with ATP, binds to GroEL and forms the GroEL/GroES complex. DnaK prevents
off-pathway reactions or stabilises certain folding intermediates. DnaJ and GrpE act as cohelpers for DnaK [41]. GroEL/ES is probably replaced by the trigger factor (TF) and DnaK,
which has already been shown by Kerner et al. [43] for E. coli or by the HrcA protein, which
is commonly found as a part of the heat-shock regulation of bacteria [44]. TF/DnaK and
HrcA are encoded in all analysed species of the Acholeplasmataceae (Figure 7). Several
Mollicutes are known to have lost groEL and groES, such as Mesoplasma florum,
Mycoplasma hyopneumoniae, Ureaplasma parvum serovar 3, Ureaplasma urealyticum,
Mycoplasma mobile and some further Mycoplasma spp. [44]. It is likely that there are even
more Mollicutes lacking these proteins. Saccardo et al. [33] suggested, based on draft
sequences, that there are four phytoplasma strains of the 16SrIII group that probably lack
GroEL/ES. The possibility that this genetic feature can be lost within the Mollicutes is
supported by experiments with transposon mutagenesis, showing that GroEL is not or only
weakly regulated during heat shock for M. genitalium or M. pneumonia [45], thereby leading
to the suggestion that this chaperone is not essential for Mycoplasma spp. in general and may
represent an evolutionary remnant. Evolutionary loss could apparently be possible due to
either the fact that GroEL is immunogenic, and therefore it would be advantageous to get rid
of it by avoiding an immune response in mammals [44] – a benefit for A. oculi when
infecting mammals – or alternatively Mollicutes possess small genomes which encode few
proteins; consequently, they own fewer substrate proteins, which have to be correctly folded
by GroEL.
Conclusions
This study demonstrated the efficiency of the SMRT approach in the complete de novo
determination of bacterial genomes. A. oculi encodes, like other Acholeplasma spp., rich
genetic content in comparison to phytoplasmas. The relatively small core genome of
phytoplasmas should be interpreted with respect to their intracellular parasitism and their
corresponding poor metabolic repertoire. In contrast, acholeplasmas depend on a richer
genetic repertoire due to their widespread distribution and colonisation of diverse microhabitats. However, for the first time, the deduced protein content of A. oculi highlights that
the loss of basic genetic elements, including the chaperone GroEL/ES and the F1FO-type Na+
ATPase system, took place in both genera of the Acholeplasmataceae. One could therefore
speculate that the common V-type H+ ATPase system in acholeplasmas may regulate the
cellular proton pool, and the V-type Na+ ATPase system may compensate for the lack of the
F1FO-type Na+ ATPase. The loss of GroEL/ES is interpreted as being not extraordinary for
Mollicutes and seems to have occurred several times within this class.
Methods
Cultivation
A. oculi strain 19L isolate was kindly provided by Jerry K. Davis (Purdue University School
of Veterinary Medicine, West Lafayette, Ind., USA) from the strain collection of the
International Organization for Mycoplasmology (IOM). Cells were cultivated in ATCC®
Medium 1039 (www.atcc.org) supplemented with 0.2% polymyxin B (Roth, Karlsruhe,
Germany) and 0.2% penicillin G (Merck, Darmstadt, Germany) at 28°C for about 14 days
and collected by centrifugation (20 min, 10,000 rpm, 4°C). The DNA isolation of A. oculi
strain 19L for SBS was performed with the DNeasy Blood & Tissue Kit (Qiagen,
Hildesheim, Germany) and according to the manufacturer’s instruction. DNA isolation
needed for preparing the PacBio 10-kb library high molecular weight genomic DNA was
performed according to Moore et al. [46].
Sequencing and assembly of SBS data
DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn,
Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA
sample preparation v2 guide, Illumina, San Diego, CA, USA). Libraries were quantified by
fluorometry, immobilised and processed onto a flow cell with a cBot followed by sequencing
by synthesis by applying TruSeq v3 chemistry on a HiSeq2500 (all components by Illumina).
The de novo assembly of the reads was performed in CLC Genomics Workbench 7.0
(www.clcbio.com). The assembly data was exported as a BAM file, indexed using SAMtools
[47] and imported in Gap5 [48]. Gaps were closed by PCR and primer-walking by applying
dye-terminator sequencing performed on an ABI 310 capillary sequencer (Life technologies,
Carlsbad, CA, USA).
Sequencing and assembly of SMRT data
A 10-kb library was prepared and processed as recommended by Pacific Biosciences
(www.smrtcommunity.com/SampleNet/Sample-Prep). Library construction and subsequent
sequencing were performed using the SMRTbell Template Preparation Reagent Kit 1.0,
DNA/Polymerase binding kit P4-C2, MagBead Kit and DNA Sequencing Kit 2.0 (all
components supplied by Pacific Biosciences, Menlo Park CA, USA.). The genome was
sequenced using PacBio RS II technology (P4-C2 chemistry). Data collected on the PacBio
RS II instrument were processed and filtered (SMRT analysis software, version 2.1). All
experiments were conducted according to the manufacturers’ instructions on a single SMRT
cell. Obtained data were analysed on the SMRT Portal V2.1.1 (www.pacb.com/devnet/) by
applying the integrated Celera® Assembler. SMRT sequencing and SBS were performed by
the Max Planck-Genome-centre Cologne, Germany (http://mpgc.mpipz.mpg.de/home/).
Identification of sequencing differences comparing both sequencing methods
Rare sequencing differences were identified via BlastN (low complexity filter off, word size
7) [49] by applying the SMRT-derived genome sequence as a reference. In addition, SBS
data were mapped onto the SMRT sequence in CLC Genomics Workbench 7.0, and PrimerBLAST [50] was used for designing oligonucleotide pairs, thus enabling the PCR
amplification of conflict regions (Table 2). Sequences of PCR products were determined by
applying dye-terminator sequencing.
Annotation of the genome sequence
The oriC region was determined through the cumulative GC-skew calculation of the
chromosome sequence in Artemis [51] and the determination of the DnaA-boxes [8]. The
adjusted genome sequence was automatically annotated in RAST [52] and annotation was
manually curated in Artemis by incorporating additional analyses obtained from the
InterProScan database [53], RNAmmer [54] and tRNAscan-SE [55]. The annotated genome
sequence of A. oculi strain 19L, including information on polymorphisms, was deposited
[EMBL:LK028559]). Read data for SBS [EMBL:ERX463488] and SMRT
[EMBL:ERX470328] were submitted to the European Nucleotide Archive
(www.ebi.ac.uk/ena/).
Prediction of orthologous proteins within the Acholeplasmataceae family
Orthologous proteins of Acholeplasmataceae were calculated by PanOCT [56] by applying
the default parameters and protein data of A. laidlawii strain PG-8A [Genbank:CP000896.1]
[8], A. brassicae strain O502 [GenBank:FO681348.1] [7], A. palmae strain J233
[GenBank:FO681347] [7], ‘Ca. P. australiense’ strain rp-A [GenBank:AM422018.1] [9] and
NZSb11 [GenBank:CP002548.1] [10], ‘Ca. P. asteris’ strain OY-M [GenBank:AP006628.2]
[11] and AY-WB [GenBank:CP000061.1] [12] and ‘Ca. P. mali’ strain AT
[GenBank:CU469464.1] [13]. The results obtained by the software were also used for the
prediction of the pan-, dispensable- and core-genome [57] of each genera and the family [58].
Phylogenetic analysis of the Acholeplasmataceae
Alignment and the phylogenetic tree were calculated for 64 16S rRNA genes of the
Acholeplasmataceae by using the maximum likelihood algorithm implemented in CLC
Genomics Workbench 7.0 and by applying the parameter ‘very accurate’ for the alignment
with a gap open cost of 10.0 and a gap extension cost of 1.0. The phylogenetic tree was
constructed by using a 1,000 bootstrapped maximum likelihood algorithm, whereby the
‘UPGMA’ construction method and the ‘Jukes Cantor’ nucleotide substitution model were
chosen. Mycoplasma genitalium strain G37 was added, in order to root the tree.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
Conceived and designed experiments: CS RR MK. Performed experiments: CS BH RR MK.
Analysed data: CS BH RR WRH BD MK. Contributed reagents/materials/analysis tools: CS
RR CB MK. Wrote the paper: CS WRH BH BD CB MK. All authors read and approved the
final manuscript.
Acknowledgements
The German Research Foundation (DFG), through projects KU 2679/2-1 and BU 890/21-1,
the German Ministry for Education and Research (BMBF, RNomics no. 01GS0805), the
Ministry of Education and Science (Republic of Serbia, Grant No. TR31043) and the German
Academic Exchange Service (DAAD/BMBF), through project 56266384, supported this
work.
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Additional files
Additional_file_1 as DOCX
Additional file 1 Number of shared proteins for each species of the Acholeplasmataceae
predicted by PanOCT. Acholeplasmas are highlighted in orange and phytoplasmas in green.
Predicted orthologs in phytoplasmas and acholeplasmas are highlighted in blue. The highest
number of shared proteins between acholeplasmas and phytoplasmas is underlined.
Abbreviations: Acholeplasma oculi, Aocu; A. laidlawii, Alai; A. palmae, Apal; A. brassicae,
Abra; ‘Candidatus Phytoplasma mali’ strain AT, Pmal; ‘Ca. P. australiense’ strain rp-A,
Paus; ‘Ca. P. australiense’ strain NZSb11, SLY; ‘Ca. P. asteris’ strain OY-M, OY-M; ‘Ca. P.
asteris’ strain AY-WB, AY-WB.
Additional_file_2 as XLSX
Additional file 2 Listed orthologous proteins of the Acholeplasmataceae and ‘unique’
proteins of Acholeplasma and ‘Candidatus Phytoplasma’. The pan analysis led to a core of
243 proteins for the family Acholeplasmataceae, to 402 ‘unique’ proteins for the genus
Acholeplasma and to 14 ‘unique’ proteins for the genus ‘Ca. Phytoplasma’, respectively.
Results were predicted by PanOCT analysis. The five completely sequenced phytoplasmas
are highlighted in green, and the four completely sequenced acholeplasmas are highlighted in
orange.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Additional files provided with this submission:
Additional file 1: 1424305861131769_add1.docx, 111K
http://www.biomedcentral.com/imedia/5809480611472839/supp1.docx
Additional file 2: 1424305861131769_add2.xlsx, 102K
http://www.biomedcentral.com/imedia/1521100291147283/supp2.xlsx